Elopomorpha (Teleostei) as a New Model Fish Group for Evolutionary Biology and Comparative Genomics

2015 ◽  
pp. 329-344 ◽  
Author(s):  
Jhen-Nien Chen ◽  
Sarah Samadi ◽  
Wei-Jen Chen
Keyword(s):  
Comparative Genomics ◽  
Evolutionary Biology ◽  
New Model ◽  
Fish Group ◽  
Model Fish

scholarly journals The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology

2012 ◽  
Vol 41 (D1) ◽  
pp. D1199-D1205 ◽  
Author(s):  
Dapeng Wang ◽  
Yan Xia ◽  
Xinna Li ◽  
Lixia Hou ◽  
Jun Yu
Keyword(s):  
Comparative Genomics ◽  
Evolutionary Biology ◽  
Rice Genome ◽  
Annotation Database

Comparative genomics and phylogenomics of Trichostrongyloidea mitochondria reveal insights for molecular diagnosis and evolutionary biology of nematode worms

Gene Reports ◽  
2017 ◽  
Vol 9 ◽  
pp. 65-73 ◽  
Author(s):  
Livia Loiola dos Santos ◽  
Francisco Prosdocimi ◽  
Nicholas Costa Barroso Lima ◽  
Igor Rodrigues da Costa ◽  
Danielle Cunha Cardoso ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Molecular Diagnosis ◽  
Evolutionary Biology

Evolutionary biology through the lens of budding yeast comparative genomics

2017 ◽  
Vol 18 (10) ◽  
pp. 581-598 ◽  
Author(s):  
Souhir Marsit ◽  
Jean-Baptiste Leducq ◽  
Éléonore Durand ◽  
Axelle Marchant ◽  
Marie Filteau ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Evolutionary Biology ◽  
Budding Yeast

scholarly journals Sinbase 2.0: An Updated Database to Study Multi-Omics in Sesamum indicum

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 272
Author(s):  
Liwen Wang ◽  
Jingyin Yu ◽  
Yanxin Zhang ◽  
Jun You ◽  
Xiurong Zhang ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Evolutionary Biology ◽  
Agronomic Traits ◽  
Genomic Variation ◽  
Functional Markers ◽  
Omics Data ◽  
Bioinformatics Analyses ◽  
Oil Crops ◽  
Large Numbers ◽  
User Friendly

Sesame is one of the oldest oil crops in the world and is widely grown in the tropical and subtropical areas of Asia, Africa and America. Upon the completion of the sesame reference genome version 1.0, we launched Sinbase 1.0 as an integrated database for genomic and bioinformatics analyses. Recently, an upgraded version (version 2.0) of the genome sequence was released. In addition, large numbers of multi-omics data have been generated on sesame, but a comprehensive database that integrates these resources for the community has been lacking until now. Here, we developed an interactive and comprehensive sesame multi-omics database, Sinbase 2.0, which provides information of the sesame updated genome containing 13 chromosomes, 3 genetic linkage maps, 5 intra- and 6 inter-species comparative genomics, 1 genomic variation analysis, 5 transcriptome data, 1 proteome, 31 functional markers, 175 putative functional genes, and 54 QTLs detected for important agronomic traits. Moreover, Sinbase 2.0 has been enriched with novel user-friendly computational tools. All datasets of Sinbase 2.0 can be downloaded online conveniently. Sinbase 2.0 will be updated regularly with new available sesame multi-omics data and can be accessed freely via Sinbase 2.—Sesame Muti-Omics Database. We expect that Sinbase 2.0, similarly to the previous version, will continue to make a major contribution to advance sesame research towards a better understanding of its biology and genetic improvement, as well as comparative genomics and evolutionary biology.

scholarly journals phyloXML: XML for evolutionary biology and comparative genomics

2009 ◽  
Vol 10 (1) ◽  
Author(s):  
Mira V Han ◽  
Christian M Zmasek
Keyword(s):  
Comparative Genomics ◽  
Evolutionary Biology

scholarly journals RecBlast: Cloud-Based Large Scale Orthology Detection

2017 ◽  
Author(s):  
Efrat Rapoport ◽  
Moran Neuhof
Keyword(s):  
Comparative Genomics ◽  
Evolutionary Biology ◽  
Large Scale ◽  
Valuable Insight ◽  
Multiple Genes ◽  
Human Genes ◽  
Amazon Web Services ◽  
Low Efficiency ◽  
Downstream Analysis ◽  
Reciprocal Blast

AbstractBackgroundThe effective detection and comparison of orthologues is crucial for answering many questions in comparative genomics, phylogenetics and evolutionary biology. One of the most common methods for discovering orthologues is widely known as ‘Reciprocal Blast’. While this method is simple when comparing only two genomes, performing a large-scale comparison of Multiple Genes across Multiple Taxa becomes a labor-intensive and inefficient task. The low efficiency of this complicated process limits the scope and breadth of questions that would otherwise benefit from this powerful method.FindingsHere we present RecBlast, an intuitive and easy-to-use pipeline that enables fast and easy discovery of orthologues along and across the evolutionary tree. RecBlast is capable of running heavy, large-scale and complex Reciprocal Blast comparisons across multiple genes and multiple taxa, in a completely automatic way. RecBlast is available as a cloud-based web server, which includes an easy-to-use user interface, implemented using cloud computing and an elastic and scalable server architecture. RecBlast is also available as a powerful standalone software supporting multi-processing for large datasets, and a cloud image which can be easily deployed on Amazon Web Services cloud. We also include sample results spanning 448 human genes, which illustrate the potential of RecBlast in detecting orthologues and in highlighting patterns and trends across multiple taxa.ConclusionsRecBlast provides a fast, inexpensive and valuable insight into trends and phenomena across distance phyla, and provides data, visualizations and directions for downstream analysis. RecBlast's fully automatic pipeline provides a new and intuitive discovery platform for researchers from any domain in biology who are interested in evolution, comparative genomics and phylogenetics, regardless of their computational skills.

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